I liked the way the story mode was handled, it enforced a sense of continuity, game everyone screen time, and not binding it with endings gave it a "life goes on after this" feel to just about everyone.
The really weird part was the beginning, where one moment there's Bayman's group being ambushed, then you're sent to Mila's gym for the first trial, then back to the ambush - might as well have mae the ambush part a prologue in attract mode or something, then start with the Mila training, then have her look at a pic of Bass, show where Bass is, go to the Rig mission, and proceed from there.
what still really weirds me out in the game is the stances for the characters that have been around longer like Kasumi and Leifang - their feet are way too far apart to make those psotures viable in combat, I wonder if tweaking them and the animation from them would mess too much with frame data for sequels.